porefile 1.0.0.9000 `(xx/03/2023)`

Refactoring. Rscripts are now in bin/ folder.
Added seqkit to environment.yml
Added reduceSilva process to remove eukaryota and phage sequences. Deactivate it with --fullSilva flag. This reduction step improves 16S classification and possibly reduces the running time a bit.
Removed seqtk in favour of seqkit for fasta/fastq manipulation.
Exposed the --headcrop and --tailcrop parameters of NanoFilt.
Synonyms mapping file now gets published in results folder.
Parameters are displayed at the begining of the run.
Nanofilt quality default is now 10 (was 8 before).
Added the Polishing workflow. Related: added megan_topPercentPolish params.
Now read assignments get published.
Removed Last, LastTrain, and Megablast workflows since added complexity to the code and any of them wasn't good enough as Minimap2 workflow.
New --help.
New README.md.
New container, now based on micromamba instead of conda.
New process GetVersions to print a file with the versions of the dependencies used (installed in the container).
Added --removeChimeras to activate chimera-removing step with (Yacrd).
Added PacBio management if user provides --minimap2_x map-pb or --minimap2_x map-hifi

porefile 0.2.2 `14/12/2022`

Minor fix in "nagual" config, which was using a "dev" tagged docker container. Now it uses the "latest".

Fixed wrong parameter documentation. "--megan_topPercent" was documented as "--megan_lcaTopPercent", so this parameter was completely ignored and the default was always used instead.
Added parameters sanity checking. This is to avoid ignoring misspelled parameters.

Merge s138: Now Porefiles only uses SILVA files, not needed MEGAN mapping files any more. Uses latest SILVA version (138.1).
Fix #12: If AutoMap returns empty, this barcode is discarded.
Added "--porechop_extra_end_trim" parameter to allow trimming n bases from the end of the amplicon in case adapters were added.
Minor improvements in error handling.
Updated documentation and scheme figure.
Updated --help